7NWH

Mammalian pre-termination 80S ribosome with eRF1 and eRF3 bound by Blasticidin S.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Blasticidin S inhibits mammalian translation and enhances production of protein encoded by nonsense mRNA.

Powers, K.T.Stevenson-Jones, F.Yadav, S.K.N.Amthor, B.Bufton, J.C.Borucu, U.Shen, D.Becker, J.P.Lavysh, D.Hentze, M.W.Kulozik, A.E.Neu-Yilik, G.Schaffitzel, C.

(2021) Nucleic Acids Res 49: 7665-7679

  • DOI: 10.1093/nar/gkab532
  • Primary Citation of Related Structures:  
    7NWG, 7NWH, 7NWI

  • PubMed Abstract: 
  • Deciphering translation is of paramount importance for the understanding of many diseases, and antibiotics played a pivotal role in this endeavour. Blasticidin S (BlaS) targets translation by binding to the peptidyl transferase center of the large ribosomal subunit ...

    Deciphering translation is of paramount importance for the understanding of many diseases, and antibiotics played a pivotal role in this endeavour. Blasticidin S (BlaS) targets translation by binding to the peptidyl transferase center of the large ribosomal subunit. Using biochemical, structural and cellular approaches, we show here that BlaS inhibits both translation elongation and termination in Mammalia. Bound to mammalian terminating ribosomes, BlaS distorts the 3'CCA tail of the P-site tRNA to a larger extent than previously reported for bacterial ribosomes, thus delaying both, peptide bond formation and peptidyl-tRNA hydrolysis. While BlaS does not inhibit stop codon recognition by the eukaryotic release factor 1 (eRF1), it interferes with eRF1's accommodation into the peptidyl transferase center and subsequent peptide release. In human cells, BlaS inhibits nonsense-mediated mRNA decay and, at subinhibitory concentrations, modulates translation dynamics at premature termination codons leading to enhanced protein production.


    Organizational Affiliation

    University of Bristol, School of Biochemistry, University Walk, Bristol BS8 1TD, UK.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L8A249Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 2
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uL4B [auth C]378Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 3
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eL31C [auth d]108Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 4
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40S ribosomal protein S3D [auth DD]281Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3
EC: 4.2.99.18
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S29E [auth dd]56Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 6
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60S ribosomal protein L5F [auth D]296Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 7
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Ribosomal protein L32G [auth e]129Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S4H [auth EE]263Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 9
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40S ribosomal protein S30I [auth ee]133Oryctolagus cuniculusMutation(s): 0 
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eL29J [auth b]226Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L6K [auth E]291Oryctolagus cuniculusMutation(s): 0 
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eL33L [auth f]110Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S5M [auth FF]204Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
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40S ribosomal protein S27aN [auth ff]68Oryctolagus cuniculusMutation(s): 0 
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uL30O [auth F]249Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 16
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60S ribosomal protein L34P [auth g]126Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S3aQ [auth BB]264Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S6R [auth GG]263Oryctolagus cuniculusMutation(s): 0 
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Epididymis tissue sperm binding protein Li 3aS [auth gg]314Oryctolagus cuniculusMutation(s): 0 
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L7aT [auth G]242Oryctolagus cuniculusMutation(s): 0 
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uL29U [auth h]123Oryctolagus cuniculusMutation(s): 0 
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S7V [auth HH]191Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S27X [auth bb]84Oryctolagus cuniculusMutation(s): 0 
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L9Y [auth H]190Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
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60S ribosomal protein L36Z [auth i]107Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 27
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40S ribosomal protein S8AA [auth II]208Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
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Eukaryotic peptide chain release factor subunit 1BA [auth ii]437Oryctolagus cuniculusMutation(s): 0 
Gene Names: ETF1ERF1RF1
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Entity ID: 29
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60S ribosomal protein L10CA [auth I]214Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL10
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Entity ID: 30
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Ribosomal protein L37DA [auth j]97Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL37
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40S ribosomal protein S9EA [auth JJ]194Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
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eRF3aFA [auth jj]428Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
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60S ribosomal protein L11GA [auth J]176Oryctolagus cuniculusMutation(s): 0 
Gene Names: ELOA
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Entity ID: 34
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L38HA [auth k]70Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
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40S ribosomal protein S10IA [auth KK]151Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
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60S ribosomal protein L13JA [auth L]211Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
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eL39KA [auth l]51Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
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40S ribosomal protein S11LA [auth LL]158Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
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Ribosomal protein L14MA [auth M]218Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL14
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Entity ID: 40
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60S RIBOSOMAL PROTEIN EL40NA [auth m]128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 41
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40S ribosomal protein S12OA [auth MM]123Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS12
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Entity ID: 42
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Ribosomal protein L15PA [auth N]204Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 43
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60s ribosomal protein l41QA [auth n]25Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein uS15RA [auth NN]150Oryctolagus cuniculusMutation(s): 0 
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60S RIBOSOMAL PROTEIN UL13SA [auth O]203Oryctolagus cuniculusMutation(s): 0 
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eL42TA [auth o]142Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 47
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uS11UA [auth OO]156Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 48
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uL22VA [auth P]199Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 49
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ribosomal protein eL43WA [auth p]109Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 50
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40S ribosomal protein uS19XA [auth PP]145Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15
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eL18YA [auth Q]188Oryctolagus cuniculusMutation(s): 0 
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eL28ZA [auth r]137Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein S16AB [auth QQ]158Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L19BB [auth R]196Oryctolagus cuniculusMutation(s): 0 
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60S acidic ribosomal protein P0CB [auth s]318Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPLP0
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40S ribosomal protein S17DB [auth RR]145Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L18aEB [auth S]176Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 58
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uL12FB [auth t]196Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 59
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40S ribosomal protein uS13GB [auth SS]152Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 60
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eL21HB [auth T]160Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL21
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Entity ID: 61
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eS19IB [auth TT]145Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 62
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L22JB [auth U]128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 63
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40S ribosomal protein S20KB [auth UU]118Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 64
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eL14LB [auth V]132Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 65
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40S ribosomal protein S21MB [auth VV]83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 66
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60S ribosomal protein L24-like proteinNB [auth W]134Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 68
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Ribosomal protein S15aPB [auth WW]139Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 69
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uL23QB [auth X]156Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein uS12SB [auth XX]142Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L26TB [auth Y]134Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL26
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Entity ID: 74
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40S ribosomal protein S24VB [auth YY]146Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L27WB [auth Z]136Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S25YB [auth ZZ]122Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L27aZB [auth a]147Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetailsImage
40S_SA_C domain-containing proteinAC [auth AA]295Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S26BC [auth aa]117Oryctolagus cuniculusMutation(s): 0 
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Find proteins for T0M5X4 (Camelus ferus)
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetailsImage
uL3CC [auth B]402Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetailsImage
eL30DC [auth c]115Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S2EC [auth CC]259Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S28FC [auth cc]69Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
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Entity ID: 23
MoleculeChainsLengthOrganismImage
mRNAW [auth hh]15Oryctolagus cuniculus
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Entity ID: 67
MoleculeChainsLengthOrganismImage
28S Ribosomal RNAOB [auth 5]3705Oryctolagus cuniculus
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Entity ID: 70
MoleculeChainsLengthOrganismImage
5S Ribosomal RNARB [auth 7]120Oryctolagus cuniculus
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Entity ID: 73
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5.8S Ribosomal RNAUB [auth 8]151Oryctolagus cuniculus
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Entity ID: 76
MoleculeChainsLengthOrganismImage
18S Ribosomal RNAXB [auth 9]1779Oryctolagus cuniculus
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GCP (Subject of Investigation/LOI)
Query on GCP

Download Ideal Coordinates CCD File 
NC [auth jj]PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
 Ligand Interaction
BLS (Subject of Investigation/LOI)
Query on BLS

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QD [auth 5]BLASTICIDIN S
C17 H26 N8 O5
CXNPLSGKWMLZPZ-ZNIXKSQXSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
GC [auth dd], HC [auth ff], IC [auth g], KN [auth aa], LC [auth j], PC [auth m], QC [auth o], TC [auth p]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AD [auth 5] , AE [auth 5] , AF [auth 5] , AG [auth 5] , AH [auth 5] , AI [auth 5] , AJ [auth 5] , AK [auth 5] , 
AD [auth 5], AE [auth 5], AF [auth 5], AG [auth 5], AH [auth 5], AI [auth 5], AJ [auth 5], AK [auth 5], AL [auth 9], AM [auth 9], AN [auth 9], BD [auth 5], BE [auth 5], BF [auth 5], BG [auth 5], BH [auth 5], BI [auth 5], BJ [auth 5], BK [auth 5], BL [auth 9], BM [auth 9], BN [auth 9], CD [auth 5], CE [auth 5], CF [auth 5], CG [auth 5], CH [auth 5], CI [auth 5], CJ [auth 5], CK [auth 5], CL [auth 9], CM [auth 9], CN [auth 9], DD [auth 5], DE [auth 5], DF [auth 5], DG [auth 5], DH [auth 5], DI [auth 5], DJ [auth 5], DK [auth 7], DL [auth 9], DM [auth 9], DN [auth 9], ED [auth 5], EE [auth 5], EF [auth 5], EG [auth 5], EH [auth 5], EI [auth 5], EJ [auth 5], EK [auth 7], EL [auth 9], EM [auth 9], EN [auth 9], FD [auth 5], FE [auth 5], FF [auth 5], FG [auth 5], FH [auth 5], FI [auth 5], FJ [auth 5], FK [auth 7], FL [auth 9], FM [auth 9], FN [auth 9], GD [auth 5], GE [auth 5], GF [auth 5], GG [auth 5], GH [auth 5], GI [auth 5], GJ [auth 5], GK [auth 7], GL [auth 9], GM [auth 9], GN [auth 9], HD [auth 5], HE [auth 5], HF [auth 5], HG [auth 5], HH [auth 5], HI [auth 5], HJ [auth 5], HK [auth 8], HL [auth 9], HM [auth 9], HN [auth 9], ID [auth 5], IE [auth 5], IF [auth 5], IG [auth 5], IH [auth 5], II [auth 5], IJ [auth 5], IK [auth 8], IL [auth 9], IM [auth 9], IN [auth 9], JC [auth hh], JD [auth 5], JE [auth 5], JF [auth 5], JG [auth 5], JH [auth 5], JI [auth 5], JJ [auth 5], JK [auth 8], JL [auth 9], JM [auth 9], JN [auth a], KC [auth hh], KD [auth 5], KE [auth 5], KF [auth 5], KG [auth 5], KH [auth 5], KI [auth 5], KJ [auth 5], KK [auth 8], KL [auth 9], KM [auth 9], LD [auth 5], LE [auth 5], LF [auth 5], LG [auth 5], LH [auth 5], LI [auth 5], LJ [auth 5], LK [auth 8], LL [auth 9], LM [auth 9], MC [auth j], MD [auth 5], ME [auth 5], MF [auth 5], MG [auth 5], MH [auth 5], MI [auth 5], MJ [auth 5], MK [auth 8], ML [auth 9], MM [auth 9], ND [auth 5], NE [auth 5], NF [auth 5], NG [auth 5], NH [auth 5], NI [auth 5], NJ [auth 5], NK [auth 8], NL [auth 9], NM [auth 9], OC [auth jj], OD [auth 5], OE [auth 5], OF [auth 5], OG [auth 5], OH [auth 5], OI [auth 5], OJ [auth 5], OK [auth 8], OL [auth 9], OM [auth 9], PD [auth 5], PE [auth 5], PF [auth 5], PG [auth 5], PH [auth 5], PI [auth 5], PJ [auth 5], PK [auth 8], PL [auth 9], PM [auth 9], QE [auth 5], QF [auth 5], QG [auth 5], QH [auth 5], QI [auth 5], QJ [auth 5], QK [auth 8], QL [auth 9], QM [auth 9], RC [auth o], RD [auth 5], RE [auth 5], RF [auth 5], RG [auth 5], RH [auth 5], RI [auth 5], RJ [auth 5], RK [auth 9], RL [auth 9], RM [auth 9], SC [auth P], SD [auth 5], SE [auth 5], SF [auth 5], SG [auth 5], SH [auth 5], SI [auth 5], SJ [auth 5], SK [auth 9], SL [auth 9], SM [auth 9], TD [auth 5], TE [auth 5], TF [auth 5], TG [auth 5], TH [auth 5], TI [auth 5], TJ [auth 5], TK [auth 9], TL [auth 9], TM [auth 9], UC [auth V], UD [auth 5], UE [auth 5], UF [auth 5], UG [auth 5], UH [auth 5], UI [auth 5], UJ [auth 5], UK [auth 9], UL [auth 9], UM [auth 9], VC [auth 5], VD [auth 5], VE [auth 5], VF [auth 5], VG [auth 5], VH [auth 5], VI [auth 5], VJ [auth 5], VK [auth 9], VL [auth 9], VM [auth 9], WC [auth 5], WD [auth 5], WE [auth 5], WF [auth 5], WG [auth 5], WH [auth 5], WI [auth 5], WJ [auth 5], WK [auth 9], WL [auth 9], WM [auth 9], XC [auth 5], XD [auth 5], XE [auth 5], XF [auth 5], XG [auth 5], XH [auth 5], XI [auth 5], XJ [auth 5], XK [auth 9], XL [auth 9], XM [auth 9], YC [auth 5], YD [auth 5], YE [auth 5], YF [auth 5], YG [auth 5], YH [auth 5], YI [auth 5], YJ [auth 5], YK [auth 9], YL [auth 9], YM [auth 9], ZC [auth 5], ZD [auth 5], ZE [auth 5], ZF [auth 5], ZG [auth 5], ZH [auth 5], ZI [auth 5], ZJ [auth 5], ZK [auth 9], ZL [auth 9], ZM [auth 9]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom210701/Z/18/Z

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-07
    Type: Initial release
  • Version 1.1: 2021-07-28
    Changes: Database references